The double-stranded RNA binding domain (dsRBD) is present in all kingdoms of life, particularly in higher eukaryotes. Growing lines of evidence indicate that proteins containing dsRBDs, a.k.a. dsRBPs, play pivotal roles in essential molecular and cellular functions, infection and immunity, and development. A key common theme of dsRBP functions is binding to structured RNA ligands via dsRBDs. While perfectly duplexed dsRNAs are typically employed as binding partners in vitro, recent studies have indicated that endogenous RNA ligands are much more diverse. However, to date, these biologically relevant in vivo RNA ligands have been examined only sporadically and in small-scale experiments, resulting in fragmentary data. In this proposal, we plan to develop experimental methods for deep sequencing RNA ligands of dsRBDs/dsRBPs in a number of commonly used cell lines and to computationally explore their sequence and structure features and biological networks. PUBLIC HEALTH RELEVANCE: Proteins that contain the double-stranded RNA binding domain (dsRBD), known as dsRBPs, have pivotal roles in both normal and pathological conditions. A critical aspect of their functions is binding to structured RNAs. These RNA partners are poorly understood. By using deep sequencing technology and bioinformatics, this project will examine and catalog the distinct populations of RNA species interacting with members of the human dsRBP family. The data will help understand the RNA-protein interactions and their roles, will predict dsRBP functions that are presently unknown, and will probably yield hitherto undiscovered RNA species.